The case of a patient who was initially diagnosed with Systemic Lupus Erythematosus, with subsequent documentation of Celiac Disease histologically and serologically is reported. The patient presented elevation of the aminotransferases, upon detection of the Celiac Disease which was initially attributed to the underlying disease. However, despite the complete resolution of her articular symptoms with a gluten-free diet, the liver chemistry abnormalities persisted. This led to consider an autoimmune hepatitis as the cause which was documented with a liver biopsy three months after the diagnosis of the celiac disease and under a strict gluten-free diet. Treatment with prednisone and azathioprine was initiated with complete normalization of aminotransferase levels. We present the sequence of events with the results and a review of the literature.